4WA9 - chain A | ABL proto-oncogene 1, non-receptor tyrosine kinase
Structure information
PDB:4WA9
PubMed:25686603
Release date:2015-02-11
Resolution:2.2 Å
 
Kinase:ABL1
Family:Abl
Group:TK
Species:HUMAN
 
Quality Score:5.6
Missing Residues:13
Missing Atoms:4
DFG conformation:out-like
αC-helix conformation:na
Salt bridge KIII.17 and EαC.24:NA
 
 
ASP rotation (xDFG.81) :121°
PHE rotation (xDFG.82) :289°
Activation loop position:-1.4Å
αC-helix position:0Å
 
G-rich loop angle:47.2°
G-rich loop distance:14Å
G-rich loop rotation:49.1°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I5
H-bond protein
Binding pocket sequence
UniprotHKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:HKLGGGQYGEVYEVAVK____________EIKPNLVQLLGV_IITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: AXI
Ligand Name: AXITINIB

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
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This ligand targets the following (sub)pockets:
Main pockets
Front

Gate

Back

Subpockets
FP-I

FP-II

BP-I-A

BP-I-B

BP-II-in

BP-II-A-in

BP-II-B-in

BP-II-out

BP-II-B

BP-III

BP-IV

BP-V

Kinase-ligand interactions
Hydrophobic Aromatic face-to-face Aromatic face-to-edge H-bond donor H-bond acceptor Ionic positive Ionic negative
I g.l II III αC
1 H
246
2 K
247
3 L
248
4 G
249
5 G
250
6 G
251
7 Q
252
8 Y
253
9 G
254
10 E
255
11 V
256
12 Y
257
13 E
258
14 V
268
15 A
269
16 V
270
17 K
271
18 _
_
19 _
_
20 _
_
αC b.l IV
21 _
_
22 _
_
23 _
_
24 _
_
25 _
_
26 _
_
27 _
_
28 _
_
29 _
_
30 E
292
31 I
293
32 K
294
33 P
296
34 N
297
35 L
298
36 V
299
37 Q
300
38 L
301
39 L
302
40 G
303
IV V GK hinge linker αD αE
41 V
304
42 _
_
43 I
313
44 I
314
45 T
315
46 E
316
47 F
317
48 M
318
49 T
319
50 Y
320
51 G
321
52 N
322
53 L
323
54 L
324
55 D
325
56 Y
326
57 L
327
58 R
328
59 E
329
60 Y
353
αE VI c.l VII VIII x
61 L
354
62 E
355
63 K
356
64 K
357
65 N
358
66 F
359
67 I
360
68 H
361
69 R
362
70 D
363
71 L
364
72 A
365
73 A
366
74 R
367
75 N
368
76 C
369
77 L
370
78 V
371
79 V
379
80 A
380
DFG a.l
81 D
381
82 F
382
83 G
383
84 L
384
85 S
385

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL1289926
Bioaffinities: 185 records for 100 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensActivin receptor type-2B5.35.35.3pKd1
Homo sapiensAdaptor-associated kinase5.75.75.9pKd2
Homo sapiensAnkyrin repeat and protein kinase domain-containing protein 15.45.45.4pKd1
Homo sapiensBMP-2-inducible protein kinase5.75.76pKd2
Homo sapiensBone morphogenetic protein receptor type-1B5.55.55.5pKd1
Homo sapiensBreakpoint cluster region protein6.76.76.7pKd2
Homo sapiensCaM-kinase kinase alpha5.95.95.9pKd1
Homo sapiensCaM-kinase kinase beta5.85.85.8pKd1
Homo sapiensCasein kinase II alpha (prime)5.65.65.6pKd1
Homo sapiensc-Jun N-terminal kinase 15.45.45.4pKd1
Homo sapiensc-Jun N-terminal kinase 3666pKd1
Homo sapiensCyclin-dependent kinase-like 26.36.36.3pKd1
Homo sapiensDiscoidin domain-containing receptor 25.35.35.3pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 15.65.65.6pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 25.65.65.6pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 56.96.96.9pKd1
Homo sapiensDual specificity protein kinase TTK5.45.45.4pKd1
Homo sapiensDual specificity testis-specific protein kinase 15.45.45.4pKd1
Homo sapiensEphrin type-B receptor 66.46.46.4pKd1
Homo sapiensEpidermal growth factor receptor erbB15.25.25.6pKd2
Homo sapiensEpithelial discoidin domain-containing receptor 16.56.56.5pKd1
Homo sapiensFibroblast growth factor receptor 16.46.46.6pKd2
Homo sapiensFibroblast growth factor receptor 17.37.37.3pKi1
Homo sapiensFibroblast growth factor receptor 2777pKd1
Homo sapiensFibroblast growth factor receptor 36.76.76.7pKd2
Homo sapiensG protein-coupled receptor kinase 45.65.65.6pKd1
Homo sapiensHepatocyte growth factor receptor666.1pKd3
Homo sapiensHormonally up-regulated neu tumor-associated kinase5.85.85.8pKd1
Homo sapiensInterferon-induced, double-stranded RNA-activated protein kinase5.15.15.1pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 15.55.55.5pKd1
Homo sapiensLeucine-rich repeat serine/threonine-protein kinase 2666pKd2
Homo sapiensMacrophage colony stimulating factor receptor7.77.77.7pKd1
Homo sapiensMisshapen-like kinase 16.36.36.3pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 125.85.85.8pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 35.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 45.35.35.3pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 95.55.55.5pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 16.56.56.5pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 25.95.95.9pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 35.95.95.9pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 45.75.76.5pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 55.65.66.3pKd2
Homo sapiensMixed lineage kinase 75.35.35.6pKd2
Homo sapiensMyosin IIIA5.75.75.7pKd1
Homo sapiensMyosin light chain kinase5.45.45.8pKd2
Homo sapiensmyosin light chain kinase 25.95.95.9pKd1
Homo sapiensNerve growth factor receptor Trk-A5.85.85.8pKd1
Homo sapiensNon-receptor tyrosine-protein kinase TNK15.75.76.8pKd2
Homo sapiensNUAK family SNF1-like kinase 25.95.95.9pKd1
Homo sapiensPlatelet-derived growth factor receptor alpha9.39.39.3pKd1
Homo sapiensPlatelet-derived growth factor receptor beta6.46.49.2pKd2
Homo sapiensProtein kinase N25.65.65.6pKd1
Homo sapiensProto-oncogene tyrosine-protein kinase MER5.55.55.5pKd1
Homo sapiensProto-oncogene tyrosine-protein kinase ROS5.55.55.5pKd1
Homo sapiensReceptor-interacting serine/threonine-protein kinase 15.65.65.6pKd1
Homo sapiensReceptor-interacting serine/threonine-protein kinase 45.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase 105.65.65.9pKd2
Homo sapiensSerine/threonine-protein kinase 166.46.46.4pKd1
Homo sapiensSerine/threonine-protein kinase 25.25.26pKd2
Homo sapiensSerine/threonine-protein kinase Aurora-A6.46.47.1pKd2
Homo sapiensSerine/threonine-protein kinase Aurora-B6.66.68pKd2
Homo sapiensSerine/threonine-protein kinase Aurora-C8.98.98.9pKd1
Homo sapiensSerine/threonine-protein kinase GAK5.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase MRCK beta5.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase MST15.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase MST25.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase PAK 45.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-15.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase PLK47.37.37.4pIC503
Homo sapiensSerine/threonine-protein kinase PLK46.16.17.8pKd2
Homo sapiensSerine/threonine-protein kinase PLK48.48.48.4pKi3
Homo sapiensSerine/threonine-protein kinase RIO15.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase RIO3666pKd1
Homo sapiensSerine/threonine-protein kinase RIPK2555pKd1
Homo sapiensSerine/threonine-protein kinase SIK15.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase SRPK15.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase SRPK35.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase ULK2555pKd1
Homo sapiensSerine/threonine-protein kinase ULK36.26.26.2pKd1
Homo sapiensSPS1/STE20-related protein kinase YSK46.66.66.6pKd1
Homo sapiensStem cell growth factor receptor8.45.49.3pKd10
Homo sapiensTRAF2- and NCK-interacting kinase5.85.86.8pKd2
Homo sapiensTyrosine kinase non-receptor protein 25.25.25.2pKd1
Homo sapiensTyrosine-protein kinase ABL8.66.89.7pIC508
Homo sapiensTyrosine-protein kinase ABL6.75.68.8pKd16
Homo sapiensTyrosine-protein kinase ABL2667.2pKd2
Homo sapiensTyrosine-protein kinase BLK5.55.55.5pKd1
Homo sapiensTyrosine-protein kinase CSK666pKd1
Homo sapiensTyrosine-protein kinase FGR5.85.86.2pKd2
Homo sapiensTyrosine-protein kinase ITK/TSK5.95.95.9pKd1
Homo sapiensTyrosine-protein kinase JAK25.55.55.5pKd2
Homo sapiensTyrosine-protein kinase JAK35.55.55.5pKd2
Homo sapiensTyrosine-protein kinase LCK5.65.65.6pKd1
Homo sapiensTyrosine-protein kinase receptor FLT36.65.67.5pKd7
Homo sapiensTyrosine-protein kinase receptor RET6.95.87pKd5
Homo sapiensTyrosine-protein kinase receptor Tie-1777pKd1
Homo sapiensTyrosine-protein kinase receptor UFO6.46.46.4pKd1
Homo sapiensTyrosine-protein kinase TIE-26.56.56.5pKd1
Homo sapiensTyrosine-protein kinase TXK5.65.65.6pKd1
Homo sapiensTyrosine-protein kinase TYK25.45.45.4pKd2
Homo sapiensTyrosine-protein kinase YES5.65.65.6pKd1
Homo sapiensVascular endothelial growth factor receptor 1101010pIC502
Homo sapiensVascular endothelial growth factor receptor 18.28.28.2pKd1
Homo sapiensVascular endothelial growth factor receptor 29.77.410pIC505
Homo sapiensVascular endothelial growth factor receptor 28.28.28.2pKd1
Homo sapiensVascular endothelial growth factor receptor 28.48.48.4pKi1
Homo sapiensVascular endothelial growth factor receptor 3101010pIC502
Homo sapiensVascular endothelial growth factor receptor 36.86.86.8pKd1